add bwa-mem2 to Dockerfile #215
Workflow file for this run
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name: testing_and_building_repo | |
on: [push, pull_request] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
name: Distribution Perl on ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
# Caching cpanm external modules | |
- name: Cache cpanm external modules | |
id: cpanmCache | |
uses: actions/cache@v3 | |
with: | |
path: ~/perl5ext | |
key: ${{ runner.os }}-build-cpanm-external | |
- name: install cpanm | |
run: | | |
wget -qO - https://cpanmin.us | /usr/bin/perl - --sudo App::cpanminus | |
# run the perl install script | |
- name: install NPG Perl dependencies, and their CPAN dependencies | |
run: | | |
cpanm --local-lib=~/perl5ext local::lib && eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib) | |
${GITHUB_WORKSPACE}/scripts/install_npg_perl_dependencies.sh $WTSI_NPG_GITHUB_URL $WTSI_NPG_BUILD_BRANCH | |
env: | |
WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg | |
WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF} | |
- name: install cpanm dependencies | |
run: | | |
eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5npg) | |
eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5ext) | |
cpanm --installdeps --notest . | |
- name: run Build.PL and ./Build | |
run: | | |
eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5ext) | |
eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5npg) | |
export TEST_AUTHOR=1 | |
perl Build.PL | |
./Build test --verbose | |
./Build install | |
# running ./Build dist and exporting files | |
- name: run ./Build dist | |
run: | | |
eval $(perl -I ~/perl5ext/lib/perl5/ -Mlocal::lib=~/perl5ext) | |
export TEST_AUTHOR=1 | |
./Build dist | |
export DIST_FILE=$(ls p4-*.tar.gz) | |
export MD5_FILE=$DIST_FILE.md5 | |
md5sum $DIST_FILE > $MD5_FILE | |
export SHA256_FILE=$DIST_FILE.sha256 | |
shasum -a 256 $DIST_FILE > $SHA256_FILE | |
# Archive logs if failure | |
- name: Archive CPAN logs | |
if: ${{ failure() }} | |
uses: actions/upload-artifact@v2 | |
with: | |
name: cpan_log | |
path: /home/runner/.cpanm/work/*/build.log | |
retention-days: 5 |